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Add initial longread QC filtering - requires filtlong module update

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This commit is contained in:
James Fellows Yates 2022-05-01 07:18:14 +02:00
parent 2bae9d58ee
commit 031cb45934
15 changed files with 233 additions and 74 deletions
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18
.github/workflows/ci.yml vendored
View file

@ -29,18 +29,18 @@ jobs:
- NXF_VER: ""
NXF_EDGE: "1"
parameters:
- "--perform_longread_clip false"
- "--perform_shortread_clipmerge false"
- "--shortread_clipmerge_tool fastp"
- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
- "--shortread_clipmerge_tool fastp --shortread_clipmerge_mergepairs"
- "--shortread_clipmerge_tool adapterremoval"
- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs --shortread_clipmerge_excludeunmerged"
- "--shortread_clipmerge_tool adapterremoval --shortread_clipmerge_mergepairs"
- "--perform_longread_qc false"
- "--perform_shortread_qc false"
- "--shortread_qc_tool fastp"
- "--shortread_qc_tool fastp --shortread_qc_mergepairs --shortread_qc_excludeunmerged"
- "--shortread_qc_tool fastp --shortread_qc_mergepairs"
- "--shortread_qc_tool adapterremoval"
- "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs --shortread_qc_excludeunmerged"
- "--shortread_qc_tool adapterremoval --shortread_qc_mergepairs"
- "--shortread_complexityfilter_tool bbduk"
- "--shortread_complexityfilter_tool prinseq"
- "--perform_runmerging"
- "--perform_runmerging --shortread_clipmerge_mergepairs"
- "--perform_runmerging --shortread_qc_mergepairs"
- "--shortread_complexityfilter false --perform_shortread_hostremoval"
steps:

2
CITATIONS.md
View file

@ -56,6 +56,8 @@
> Buchfink, Benjamin, Chao Xie, and Daniel H. Huson. 2015. “Fast and Sensitive Protein Alignment Using DIAMOND.” Nature Methods 12 (1): 59-60. doi: 10.1038/nmeth.3176.
- [FILTLONG](https://github.com/rrwick/Filtlong)
## Software packaging/containerisation tools
- [Anaconda](https://anaconda.com)

48
conf/modules.config
View file

@ -51,10 +51,10 @@ process {
withName: FASTP_SINGLE {
ext.args = [
// trimming options
params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "",
params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
// filtering options
"--length_required ${params.shortread_clipmerge_minlength}"
"--length_required ${params.shortread_qc_minlength}"
].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
@ -68,13 +68,13 @@ process {
withName: FASTP_PAIRED {
ext.args = [
// collapsing options - option to retain singletons
params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
params.shortread_qc_excludeunmerged ? '' : "--include_unmerged",
// trimming options
params.shortread_clipmerge_skipadaptertrim ? "--disable_adapter_trimming" : "",
params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : "--detect_adapter_for_pe",
params.shortread_qc_skipadaptertrim ? "--disable_adapter_trimming" : "",
params.shortread_qc_adapter1 ? "--adapter_sequence ${params.shortread_qc_adapter1}" : "",
params.shortread_qc_adapter2 ? "--adapter_sequence_r2 ${params.shortread_qc_adapter2}" : "--detect_adapter_for_pe",
// filtering options
"--length_required ${params.shortread_clipmerge_minlength}"
"--length_required ${params.shortread_qc_minlength}"
].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
@ -88,10 +88,10 @@ process {
withName: ADAPTERREMOVAL_SINGLE {
ext.args = [
// trimming options
params.shortread_clipmerge_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
params.shortread_clipmerge_adapter1 ? "--adapter1 ${params.shortread_clipmerge_adapter1}" : "",
params.shortread_qc_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
params.shortread_qc_adapter1 ? "--adapter1 ${params.shortread_qc_adapter1}" : "",
// filtering options
"--minlength ${params.shortread_clipmerge_minlength}"
"--minlength ${params.shortread_qc_minlength}"
].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
@ -105,13 +105,13 @@ process {
withName: ADAPTERREMOVAL_PAIRED {
ext.args = [
// collapsing options
params.shortread_clipmerge_mergepairs ? "--collapse" : "",
params.shortread_qc_mergepairs ? "--collapse" : "",
// trimming options
params.shortread_clipmerge_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
params.shortread_clipmerge_adapter1 ? "--adapter1 ${params.shortread_clipmerge_adapter1}" : "",
params.shortread_clipmerge_adapter2 ? "--adapter2 ${params.shortread_clipmerge_adapter2}" : "",
params.shortread_qc_skipadaptertrim ? "--adapter1 '' --adapter2 ''" : "",
params.shortread_qc_adapter1 ? "--adapter1 ${params.shortread_qc_adapter1}" : "",
params.shortread_qc_adapter2 ? "--adapter2 ${params.shortread_qc_adapter2}" : "",
// filtering options
"--minlength ${params.shortread_clipmerge_minlength}"
"--minlength ${params.shortread_qc_minlength}"
].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
@ -132,6 +132,22 @@ process {
]
}
withName: FILTLONG {
ext.args = [
"--min_length ${params.longread_qc_minlength}",
"--keep_percent ${params.longread_qc_keepbppercent}",
"--target_bases ${params.longread_qc_targetnbases}"
]
.join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [
path: { "${params.outdir}/porechop" },
mode: params.publish_dir_mode,
pattern: '*.fastq.gz',
enabled: params.save_preprocessed_reads
]
}
withName: BOWTIE2_BUILD {
publishDir = [
path: { "${params.outdir}/bowtie2/build" },

4
conf/test.config
View file

@ -24,8 +24,8 @@ params {
// TODO nf-core: Give any required params for the test so that command line flags are not needed
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/samplesheet.csv'
databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
perform_shortread_clipmerge = true
perform_longread_clip = false
perform_shortread_qc = true
perform_longread_qc = false
perform_shortread_complexityfilter = true
perform_shortread_hostremoval = true
shortread_hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'

10
docs/usage.md
View file

@ -162,16 +162,16 @@ nf-core/taxprofiler offers four main preprocessing steps
#### Read Processing
Raw sequencing read processing in the form of adapter clipping and paired-end read merging can be activated via the `--perform_shortread_clipmerge` or `--perform_longread_clip` flags.
Raw sequencing read processing in the form of adapter clipping and paired-end read merging can be activated via the `--perform_shortread_qc` or `--perform_longread_qc` flags.
It is highly recommended to run this on raw reads to remove artefacts from sequencing that can cause false positive identification of taxa (e.g. contaminated reference genomes) and/or skews in taxonomic abundance profiles.
There are currently two options for short-read preprocessing: `fastp` or `adapterremoval`.
For adapter clipping, you can either rely on tool default adapter sequences, or supply your own adapters (`--shortread_clipmerge_adapter1` and `--shortread_clipmerge_adapter2`)
By default, paired-end merging is not activated and paired-end profiling is performed where supported otherwise pairs will be independently profiled. If paired-end merging is activated you can also specify whether to exclude unmerged reads in the reads sent for profiling (`--shortread_clipmerge_mergepairs` and `--shortread_clipmerge_excludeunmerged`).
You can also turn off clipping and only perform paired-end merging, if requested. This can be useful when processing data downloaded from the ENA, SRA, or DDBJ (`--shortread_clipmerge_skipadaptertrim`).
Both tools support length filtering of reads and can be tuned with `--shortread_clipmerge_minlength`. Performing length filtering can be useful to remove short (often low sequencing complexity) sequences that result in unspecific classification and therefore slow down runtime during profiling, with minimal gain.
For adapter clipping, you can either rely on tool default adapter sequences, or supply your own adapters (`--shortread_qc_adapter1` and `--shortread_qc_adapter2`)
By default, paired-end merging is not activated and paired-end profiling is performed where supported otherwise pairs will be independently profiled. If paired-end merging is activated you can also specify whether to exclude unmerged reads in the reads sent for profiling (`--shortread_qc_mergepairs` and `--shortread_qc_excludeunmerged`).
You can also turn off clipping and only perform paired-end merging, if requested. This can be useful when processing data downloaded from the ENA, SRA, or DDBJ (`--shortread_qc_skipadaptertrim`).
Both tools support length filtering of reads and can be tuned with `--shortread_qc_minlength`. Performing length filtering can be useful to remove short (often low sequencing complexity) sequences that result in unspecific classification and therefore slow down runtime during profiling, with minimal gain.
There is currently one option for long-read Oxford Nanopore processing: `porechop`.

3
modules.json
View file

@ -36,6 +36,9 @@
"fastqc": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"filtlong": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"kaiju/kaiju": {
"git_sha": "8856f127c58f6af479128be8b8df4d42e442ddbe"
},

36
modules/nf-core/modules/filtlong/main.nf generated Normal file
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@ -0,0 +1,36 @@
process FILTLONG {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::filtlong=0.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0' :
'quay.io/biocontainers/filtlong:0.2.1--h9a82719_0' }"
input:
tuple val(meta), path(shortreads), path(longreads)
output:
tuple val(meta), path("${meta.id}_lr_filtlong.fastq.gz"), emit: reads
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def short_reads = meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
"""
filtlong \\
$short_reads \\
$args \\
$longreads \\
| gzip -n > ${prefix}_lr_filtlong.fastq.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
filtlong: \$( filtlong --version | sed -e "s/Filtlong v//g" )
END_VERSIONS
"""
}

50
modules/nf-core/modules/filtlong/meta.yml generated Normal file
View file

@ -0,0 +1,50 @@
name: filtlong
description: Filtlong filters long reads based on quality measures or short read data.
keywords:
- nanopore
- quality control
- QC
- filtering
- long reads
- short reads
tools:
- filtlong:
description: Filtlong is a tool for filtering long reads. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
homepage: https://anaconda.org/bioconda/filtlong
documentation: None
tool_dev_url: https://github.com/rrwick/Filtlong
doi: ""
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- shortreads:
type: file
description: fastq file
pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
- longreads:
type: file
description: fastq file
pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- reads:
type: file
description: Filtered (compressed) fastq file
pattern: "*.fastq.gz"
authors:
- "@d4straub"

28
nextflow.config
View file

@ -55,16 +55,23 @@ params {
databases = null
// FASTQ preprocessing
perform_shortread_clipmerge = false
shortread_clipmerge_tool = 'fastp'
shortread_clipmerge_skipadaptertrim = false
shortread_clipmerge_mergepairs = false
shortread_clipmerge_excludeunmerged = false
shortread_clipmerge_adapter1 = null
shortread_clipmerge_adapter2 = null
shortread_clipmerge_minlength = 15
perform_longread_clip = false
save_preprocessed_reads = false
perform_shortread_qc = false
shortread_qc_tool = 'fastp'
shortread_qc_skipadaptertrim = false
shortread_qc_mergepairs = false
shortread_qc_excludeunmerged = false
shortread_qc_adapter1 = null
shortread_qc_adapter2 = null
shortread_qc_minlength = 15
perform_longread_qc = false
longread_qc_run_clip = false
longread_qc_run_filter = false
longread_qc_minlength = 1000
longread_qc_keepbppercent = 90
longread_qc_targetnbases = 500000000
save_preprocessed_reads = false
// Complexity filtering
perform_shortread_complexityfilter = false
@ -185,6 +192,7 @@ profiles {
}
// Load igenomes.config if required
if (!params.igenomes_ignore) {
includeConfig 'conf/igenomes.config'
} else {

36
nextflow_schema.json
View file

@ -262,7 +262,7 @@
"type": "string",
"default": "None"
},
"shortread_clipmerge_excludeunmerged": {
"shortread_qc_excludeunmerged": {
"type": "boolean"
},
"run_malt": {
@ -291,26 +291,26 @@
"type": "boolean",
"description": "Enable MetaPhlAn for taxonomic profiling"
},
"shortread_clipmerge_tool": {
"shortread_qc_tool": {
"type": "string",
"default": "fastp",
"enum": ["fastp", "adapterremoval"]
},
"shortread_clipmerge_skipadaptertrim": {
"shortread_qc_skipadaptertrim": {
"type": "boolean"
},
"shortread_clipmerge_mergepairs": {
"shortread_qc_mergepairs": {
"type": "boolean"
},
"shortread_clipmerge_adapter1": {
"shortread_qc_adapter1": {
"type": "string",
"default": "None"
},
"shortread_clipmerge_adapter2": {
"shortread_qc_adapter2": {
"type": "string",
"default": "None"
},
"shortread_clipmerge_minlength": {
"shortread_qc_minlength": {
"type": "integer",
"default": 15
},
@ -347,10 +347,10 @@
"save_runmerged_reads": {
"type": "boolean"
},
"perform_shortread_clipmerge": {
"perform_shortread_qc": {
"type": "boolean"
},
"perform_longread_clip": {
"perform_longread_qc": {
"type": "boolean"
},
"perform_shortread_complexityfilter": {
@ -397,6 +397,24 @@
"type": "string",
"default": "tsv",
"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"]
},
"longread_qc_run_clip": {
"type": "boolean"
},
"longread_qc_run_filter": {
"type": "boolean"
},
"longread_qc_minlength": {
"type": "integer",
"default": 1000
},
"longread_qc_keepbppercent": {
"type": "integer",
"default": 90
},
"longread_qc_targetnbases": {
"type": "integer",
"default": 500000000
}
}
}

45
subworkflows/local/longread_preprocessing.nf
View file

@ -4,6 +4,7 @@
include { FASTQC as FASTQC_PROCESSED } from '../../modules/nf-core/modules/fastqc/main'
include { PORECHOP } from '../../modules/nf-core/modules/porechop/main'
include { FILTLONG } from '../../modules/nf-core/modules/filtlong/main'
workflow LONGREAD_PREPROCESSING {
take:
@ -13,21 +14,43 @@ workflow LONGREAD_PREPROCESSING {
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
PORECHOP ( reads )
if ( params.longread_qc_run_clip && !params.longread_qc_run_filter ) {
PORECHOP ( reads )
ch_processed_reads = PORECHOP.out.reads
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
}
ch_processed_reads = PORECHOP.out.reads
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
FASTQC_PROCESSED ( PORECHOP.out.reads )
ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
}
} else if ( !params.longread_qc_run_clip && params.longread_qc_run_filter ) {
ch_processed_reads = FILTLONG ( reads.map{ meta, reads -> [meta, [], reads ]} )
ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
} else {
PORECHOP ( reads )
ch_clipped_reads = PORECHOP.out.reads
.map {
meta, reads ->
def meta_new = meta.clone()
meta_new['single_end'] = 1
[ meta_new, reads ]
}
ch_processed_reads = FILTLONG ( ch_clipped_reads.map{ meta, reads -> [meta, [], reads ]} ).reads
ch_versions = ch_versions.mix(PORECHOP.out.versions.first())
ch_versions = ch_versions.mix(FILTLONG.out.versions.first())
}
FASTQC_PROCESSED ( ch_processed_reads.dump(tag: "filtlong") )
ch_multiqc_files = ch_multiqc_files.mix( FASTQC_PROCESSED.out.zip )
emit:
reads = ch_processed_reads // channel: [ val(meta), [ reads ] ]
versions = ch_versions // channel: [ versions.yml ]

4
subworkflows/local/shortread_adapterremoval.nf
View file

@ -29,7 +29,7 @@ workflow SHORTREAD_ADAPTERREMOVAL {
* has to be exported in a separate channel and we must manually recombine when necessary.
*/
if ( params.shortread_clipmerge_mergepairs && !params.shortread_clipmerge_excludeunmerged ) {
if ( params.shortread_qc_mergepairs && !params.shortread_qc_excludeunmerged ) {
ch_concat_fastq = Channel.empty()
.mix(
@ -54,7 +54,7 @@ workflow SHORTREAD_ADAPTERREMOVAL {
ch_adapterremoval_reads_prepped = CAT_FASTQ.out.reads
.mix(ADAPTERREMOVAL_SINGLE.out.singles_truncated)
} else if ( params.shortread_clipmerge_mergepairs && params.shortread_clipmerge_excludeunmerged ) {
} else if ( params.shortread_qc_mergepairs && params.shortread_qc_excludeunmerged ) {
ch_concat_fastq = Channel.empty()
.mix(

4
subworkflows/local/shortread_fastp.nf
View file

@ -21,9 +21,9 @@ workflow SHORTREAD_FASTP {
FASTP_SINGLE ( ch_input_for_fastp.single, false, false )
// Last parameter here turns on merging of PE data
FASTP_PAIRED ( ch_input_for_fastp.paired, false, params.shortread_clipmerge_mergepairs )
FASTP_PAIRED ( ch_input_for_fastp.paired, false, params.shortread_qc_mergepairs )
if ( params.shortread_clipmerge_mergepairs ) {
if ( params.shortread_qc_mergepairs ) {
ch_fastp_reads_prepped_pe = FASTP_PAIRED.out.reads_merged
.map {
meta, reads ->

4
subworkflows/local/shortread_preprocessing.nf
View file

@ -15,11 +15,11 @@ workflow SHORTREAD_PREPROCESSING {
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
if ( params.shortread_clipmerge_tool == "fastp" ) {
if ( params.shortread_qc_tool == "fastp" ) {
ch_processed_reads = SHORTREAD_FASTP ( reads ).reads
ch_versions = ch_versions.mix( SHORTREAD_FASTP.out.versions )
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_FASTP.out.mqc )
} else if ( params.shortread_clipmerge_tool == "adapterremoval" ) {
} else if ( params.shortread_qc_tool == "adapterremoval" ) {
ch_processed_reads = SHORTREAD_ADAPTERREMOVAL ( reads ).reads
ch_versions = ch_versions.mix( SHORTREAD_ADAPTERREMOVAL.out.versions )
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_ADAPTERREMOVAL.out.mqc )

15
workflows/taxprofiler.nf
View file

@ -19,8 +19,11 @@ for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true
// Check mandatory parameters
if (params.input ) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' }
if (params.databases) { ch_databases = file(params.databases) } else { exit 1, 'Input database sheet not specified!' }
if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-reads. Pairs will be profiled as separate files."
if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
if (params.shortread_qc_mergepairs && params.run_malt ) log.warn "[nf-core/taxprofiler] MALT does not accept uncollapsed paired-short reads. Pairs will be profiled as separate files."
if (params.shortread_qc_excludeunmerged && !params.shortread_qc_mergepairs) exit 1, "ERROR: [nf-core/taxprofiler] cannot include unmerged reads when merging not turned on. Please specify --shortread_qc_mergepairs"
if ( (params.longread_qc_run_clip || params.longread_qc_run_filter) & !params.perform_longread_qc ) exit 1, "ERROR: [nf-core/taxprofiler] --longread_qc_run_clip or --longread_qc_run_filter requested but quality-control not turned on. Please specify --perform_long_qc"
if (params.perform_shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
if (!params.shortread_hostremoval_reference && params.shortread_hostremoval_reference_index) { exit 1, "ERROR: [nf-core/taxprofiler] --shortread_hostremoval_index provided but no --shortread_hostremoval_reference FASTA supplied. Check input." }
@ -110,14 +113,14 @@ workflow TAXPROFILER {
/*
SUBWORKFLOW: PERFORM PREPROCESSING
*/
if ( params.perform_shortread_clipmerge ) {
if ( params.perform_shortread_qc ) {
ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads
ch_versions = ch_versions.mix( SHORTREAD_PREPROCESSING.out.versions )
} else {
ch_shortreads_preprocessed = INPUT_CHECK.out.fastq
}
if ( params.perform_longread_clip ) {
if ( params.perform_longread_qc ) {
ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads
.map { it -> [ it[0], [it[1]] ] }
ch_versions = ch_versions.mix( LONGREAD_PREPROCESSING.out.versions )
@ -211,11 +214,11 @@ workflow TAXPROFILER {
ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
if (params.perform_shortread_clipmerge) {
if (params.perform_shortread_qc) {
ch_multiqc_files = ch_multiqc_files.mix( SHORTREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
}
if (params.perform_longread_clip) {
if (params.perform_longread_qc) {
ch_multiqc_files = ch_multiqc_files.mix( LONGREAD_PREPROCESSING.out.mqc.collect{it[1]}.ifEmpty([]) )
}